I own PTGui Pro and CS6. For simple and easy to align images ptgui will suffice but for anything with complex situations, i.e. difficult to assign control points, or super large with multi-laters PS6 has a much better stitching engine.

If you already have PS6 and you are not getting results you are happy with then you might want to learn the software a little better. There are several auto align selections and each one is tailored to a specific type of panorama and depending on lens characteristics one may perform better then another.

IMO PS6 is the best one out there and I have demoed several and have extensive experience with PTGui Pro. Nice thing is PTGui is cheap.

I shoot quite a number of panoramic images. After much research and dabbling with several, I settled on PtGui as well. The interface is stupid easy, it processes images crazy fast, and the results are flawless. I shoot using a Manfrotto 303sph head at times, but I also shoot quite a number freehand. It deals with each type with equal aplomb. Some of my work has been printed from these files on metal prints at 4'x8'. One commercial application printed one panorama at 22' in length. They look beautiful. Here are some samples to show how well the software deals with overlap/edges. There was NO manipulation done to the software results.

Windows ICE is fast and does a fairly good job. Just dump the photos into it and rather quickly it will make the pano, disregarding photos that don't belong. For online viewing, you can upload the panos to Photosynth. I've recently done some interior panos of an old 19th century coastal defense fort (Ft. Barrancas) in Pensacola. Magic Lantern to take the photos (auto HDR), Lightroom to stack and blend the images. I find that the blended images usually need some enhancement after blending and it's easy to stay in Lightoom and do that. I use ICE to make the pano and upload to Photsynth.

photosynth.net/search.aspx I post as 'emag325'

Hugin is my second choice, it does an excellent job but is far slower. It's a good front end for much of the software useful for panos.

I'm strictly a hobbyist and most of my work is done on a Vista laptop, those of you with more powerful computers will likely find other methods that work well for you.

Like most aspects of photography, this is one where you can take many paths to get to various flavors of your destination.